Mixed modeling with genetic relationship matrices
Effect-size plot
Bayesian false-discovery probability
Score statistics for association of traits with haplotypes
Functions for single nucleotide polymorphisms (SNPs)
Bradley-Terry model for contingency table
Gene counting for haplotype analysis
Power and sample size for case-cohort design
forest plot as R/meta's forest for METAL outputs
Multivariate meta-analysis based on generalized least squares
A function to prepare pedigrees in post-MAKEPED format
Haplotype frequency estimation based on a genotype table of two multiallelic markers
Power for population-based association design
False-positive report probability
Truncated Manhattan plot
score statistics for testing genetic linkage of quantitative trait
Heritability estimation according to twin correlations
Kinship coefficient and genetic index of familiality
Chow's test for heterogeneity in two regressions
Regional association plot
Manhattan plot with annotations
Obtain correlation coefficients and their variance-covariances
Haplotype trend regression
Test/Power calculation for mediating effect
Sample size for family-based linkage and association design
Genetic analysis package
A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies
LD statistics for two multiallelic markers
Gene counting for haplotype analysis
Hardy-Weinberg equilibrium test using MCMC
genomic control based on p values
Permutation tests using GENECOUNTING
genomic control
Hardy-Weinberg equlibrium test for a multiallelic marker
Gene counting for haplotype analysis
Q-Q plot for uniformly distributed random variable
Transmission/disequilibrium test of a multiallelic marker
Sentinel identification from GWAS summary statistics
multiple imputation analysis for hap
Statistics for 2 by K table
A utility function to read ms output
Preparing weight for GENECOUNTING
Probability of familial clustering of disease
Sample size calculation for mediation analysis
Power for case-control association design
Heritability estimation based on genomic relationship matrix using JAGS
Meta-analysis of p values
Internal functions for gap
Haplotype reconstruction
Manhattan plot
Fixed and random effects model for meta-analysis
Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS
Converting pedigree(s) to dot file(s)
kinship matrix for simple pedigree
Probability of familial clustering of disease
Plot haplotype frequencies versus haplotype score statistics
Means and variances under 1- and 2- locus (biallelic) QTL model
Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model
Quantile-comparison plots
Print a hap.score object
Power calculation for two-stage case-control design
Whittemore-Halpern scores for allele-sharing
LD statistics for two diallelic markers
AE model using nuclear family trios